1 SBW comparison of CASAL and Casal2 model configurations

This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 8 Casal2 model configurations (3 BetaDiff, 2 CppAD, and 3 ADOL-C).

The CASAL model sensitivity 1 has a smaller minimisation tolerance value than the CASAL base model (1e-8 vs. 2e-6).

The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-8 vs. 2e-6). The Casal2 CppAD models have a tolerance value of 1e-9.

1.1 SBW model characteristics

The main characteristics of the Test Case SBW (southern blue whiting) CASAL model are:

  • one stock, ages 2 - 15
  • two areas, spawn and nospawn
  • years 1960 - 2015, projection years 2016 - 2021
  • two time steps
  • two stock categories, male and female
  • sex-specific migration from 'nospawn' to 'spawn'
  • male and female natural mortality (M) average of 0.2, difference of 0.02
  • Beverton-Holt stock-recruitment relationship, with steepness (h) 0.9 and \(\sigma_R\) 1.0
  • length-weight relationship (\(W = aL^b\))
  • no ageing error
  • one fishery in area 'spawn'

Observation data include:

  • empirical sex-specific length-at-age data for 1979 - 2015
  • survey indices for immature and mature partitions
  • fishery sex-specific proportions-at-age

Parameters estimated include:

  • B0
  • process error for the mature survey index
  • the average of and difference between male and female natural mortality
  • sex-specific migration rates
  • YCS (recruitment deviations)

1.2 R environment

## [1] "Mon Nov 23 15:50:01 2020"
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
## 
## locale:
##  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8    
##  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8   
##  [7] LC_PAPER=en_GB.UTF_8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] casal2_1.0     casal_2.30     ggthemes_4.2.0 ggmcmc_1.5.0   tidyr_1.1.2   
##  [6] ggplot2_3.3.2  gridExtra_2.3  coda_0.19-4    rlist_0.4.6.1  huxtable_5.1.1
## [11] dplyr_1.0.2    plyr_1.8.6     devtools_2.3.2 usethis_1.6.3 
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_1.1.0   xfun_0.19          remotes_2.2.0      purrr_0.3.4       
##  [5] lattice_0.20-38    colorspace_1.4-1   vctrs_0.3.5        generics_0.1.0    
##  [9] testthat_2.3.2     htmltools_0.5.0    yaml_2.2.1         rlang_0.4.8       
## [13] pkgbuild_1.1.0     pillar_1.4.7       glue_1.4.2         withr_2.3.0       
## [17] RColorBrewer_1.1-2 sessioninfo_1.1.1  lifecycle_0.2.0    stringr_1.4.0     
## [21] munsell_0.5.0      gtable_0.3.0       memoise_1.1.0      evaluate_0.14     
## [25] GGally_1.4.0       knitr_1.30         callr_3.5.1        ps_1.4.0          
## [29] fansi_0.4.1        Rcpp_1.0.5         scales_1.1.1       desc_1.2.0        
## [33] pkgload_1.1.0      fs_1.5.0           digest_0.6.27      stringi_1.5.3     
## [37] processx_3.4.4     rprojroot_2.0.2    grid_3.6.0         cli_2.2.0         
## [41] tools_3.6.0        magrittr_2.0.1     tibble_3.0.4       crayon_1.3.4      
## [45] pkgconfig_2.0.3    ellipsis_0.3.1     data.table_1.13.2  prettyunits_1.1.1 
## [49] reshape_0.8.8      assertthat_0.2.1   rmarkdown_2.5      R6_2.5.0          
## [53] compiler_3.6.0

1.3 CASAL and Casal2 model output

source('../../R-functions/report_read_in_CASAL_MPD_files.R')
source('../../R-functions/report_read_in_Casal2_MPD_files.R')
## Warning in sqrt(1/diag(V)): NaNs produced
## Warning in cov2cor(data): diag(.) had 0 or NA entries; non-finite result is
## doubtful
## Warning in sqrt(1/diag(V)): NaNs produced
## Warning in cov2cor(data): diag(.) had 0 or NA entries; non-finite result is
## doubtful

1.4 Tables

Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results

CASAL parameter estimates
rownamesBase_ModelSensitivity_1Percent_Diff
initialization.B0              314500.00000314500.000000.000
relative_abundance[TangaroaAcousticMature].cv_process_error0.000100.000100.000
natural_mortality.avg             0.155800.155800.000
natural_mortality.diff            -0.00914-0.009140.000
migration[toSpawn].rates_male1     0.085580.085580.000
migration[toSpawn].rates_male2     0.729900.729900.000
migration[toSpawn].rates_male3     0.512700.512700.000
migration[toSpawn].rates_male4     0.331200.331200.000
migration[toSpawn].rates_male5     0.990000.990000.000
migration[toSpawn].rates_female1   0.019070.019070.000
migration[toSpawn].rates_female2   0.512500.512500.000
migration[toSpawn].rates_female3   0.941200.941200.000
migration[toSpawn].rates_female4   0.999000.999000.000
migration[toSpawn].rates_female5   0.990000.990000.000
recruitment.YCS1            0.255900.255900.000
recruitment.YCS2            0.261000.261000.000
recruitment.YCS3            0.267000.267000.000
recruitment.YCS4            0.274300.274300.000
recruitment.YCS5            0.283200.283200.000
recruitment.YCS6            0.294100.294100.000
recruitment.YCS7            0.308800.308800.000
recruitment.YCS8            0.824700.824700.000
recruitment.YCS9            0.531600.531600.000
recruitment.YCS10           0.370700.370700.000
recruitment.YCS11           0.266800.266800.000
recruitment.YCS12           0.138500.138500.000
recruitment.YCS13           0.080250.080250.000
recruitment.YCS14           0.158200.158200.000
recruitment.YCS15           0.106300.106300.000
recruitment.YCS16           0.057570.057570.000
recruitment.YCS17           0.060790.060790.000
recruitment.YCS18           0.127200.127200.000
recruitment.YCS19           0.050570.050570.000
recruitment.YCS20           0.039590.039590.000
recruitment.YCS21           0.049960.049960.000
recruitment.YCS22           0.375900.375900.000
recruitment.YCS23           0.368200.368200.000
recruitment.YCS24           0.094020.094020.000
recruitment.YCS25           0.032800.032800.000
recruitment.YCS26           0.136500.136500.000
recruitment.YCS27           0.130800.130800.000
recruitment.YCS28           0.112600.112600.000
recruitment.YCS29           0.286200.286200.000
recruitment.YCS30           0.127900.127900.000
recruitment.YCS31           0.437700.437700.000
recruitment.YCS32           0.035900.035900.000
recruitment.YCS33           0.256500.256500.000
recruitment.YCS34           2.751002.751000.000
recruitment.YCS35           0.558700.558700.000
recruitment.YCS36           0.263900.263900.000
recruitment.YCS37           0.126700.126700.000
recruitment.YCS38           0.560000.560000.000
recruitment.YCS39           0.361900.361900.000
recruitment.YCS40           0.144900.144900.000
recruitment.YCS41           0.320600.320600.000
recruitment.YCS42           0.192800.192800.000
recruitment.YCS43           0.298700.298700.000
recruitment.YCS44           0.705200.705200.000
recruitment.YCS45           0.417700.417700.000
recruitment.YCS46           0.254300.254300.000
recruitment.YCS47           0.252400.252400.000
recruitment.YCS48           0.325000.325000.000
recruitment.YCS49           1.696001.696000.000
recruitment.YCS50           0.686600.686600.000
recruitment.YCS51           0.200700.200700.000
recruitment.YCS52           1.204001.204000.000
recruitment.YCS53           0.169300.169300.000
recruitment.YCS54           0.875700.875700.000
recruitment.YCS55           0.132700.132700.000
recruitment.YCS56           1.000001.000000.000
Casal2 parameter estimates
rownamesbetadiff_casal_flags_onbetadiff_casal_flags_offbetadiff_casal_flags_on_low_tolcppad_casal_flags_oncppad_casal_flags_offadolc_casal_flags_onadolc_casal_flags_offadolc_casal_flags_on_low_tol
process[Recruitment].b0              299610.00000299610.00000299610.00000314527.00000314527.00000299610.00000299610.00000299610.00000
selectivity[MaturationSel_male].v{1}            0.085370.085370.085370.085580.085580.085370.085370.08537
selectivity[MaturationSel_male].v{2}            0.735260.735260.735260.729930.729930.735260.735260.73526
selectivity[MaturationSel_male].v{3}            0.514320.514320.514320.512670.512670.514320.514320.51432
selectivity[MaturationSel_male].v{4}            0.293980.293980.293980.331180.331180.293980.293980.29398
selectivity[MaturationSel_female].v{1}            0.019030.019030.019030.019070.019070.019030.019030.01903
selectivity[MaturationSel_female].v{2}            0.515640.515640.515640.512540.512540.515640.515640.51564
selectivity[MaturationSel_female].v{3}            0.945780.945780.945780.941200.941200.945780.945780.94578
selectivity[MaturationSel_female].v{4}            0.999000.999000.999000.999000.999000.999000.999000.99900
process[Recruitment].ycs_values{1958}0.251690.251690.251690.255900.255900.251690.251690.25169
process[Recruitment].ycs_values{1959}0.256260.256260.256260.260990.260990.256260.256260.25626
process[Recruitment].ycs_values{1960}0.261700.261700.261700.267020.267020.261700.261700.26170
process[Recruitment].ycs_values{1961}0.268300.268300.268300.274310.274310.268300.268300.26830
process[Recruitment].ycs_values{1962}0.276320.276320.276320.283170.283170.276320.276320.27632
process[Recruitment].ycs_values{1963}0.286360.286360.286360.294100.294100.286360.286360.28636
process[Recruitment].ycs_values{1964}0.300090.300090.300090.308800.308800.300090.300090.30009
process[Recruitment].ycs_values{1965}0.707010.707010.707010.824680.824680.707010.707010.70701
process[Recruitment].ycs_values{1966}0.464020.464020.464020.531620.531620.464020.464020.46402
process[Recruitment].ycs_values{1967}0.322370.322370.322370.370700.370700.322370.322370.32237
process[Recruitment].ycs_values{1968}0.231720.231720.231720.266760.266760.231720.231720.23172
process[Recruitment].ycs_values{1969}0.121430.121430.121430.138530.138530.121430.121430.12143
process[Recruitment].ycs_values{1970}0.070840.070840.070840.080250.080250.070840.070840.07084
process[Recruitment].ycs_values{1971}0.136120.136120.136120.158220.158220.136120.136120.13612
process[Recruitment].ycs_values{1972}0.091510.091510.091510.106300.106300.091510.091510.09151
process[Recruitment].ycs_values{1973}0.049830.049830.049830.057570.057570.049830.049830.04983
process[Recruitment].ycs_values{1974}0.052150.052150.052150.060790.060790.052150.052150.05215
process[Recruitment].ycs_values{1975}0.107500.107500.107500.127250.127250.107500.107500.10750
process[Recruitment].ycs_values{1976}0.043080.043080.043080.050570.050570.043080.043080.04308
process[Recruitment].ycs_values{1977}0.033730.033730.033730.039590.039590.033730.033730.03373
process[Recruitment].ycs_values{1978}0.042270.042270.042270.049960.049960.042270.042270.04227
process[Recruitment].ycs_values{1979}0.312770.312770.312770.375870.375870.312770.312770.31277
process[Recruitment].ycs_values{1980}0.304800.304800.304800.368160.368160.304800.304800.30480
process[Recruitment].ycs_values{1981}0.077990.077990.077990.094020.094020.077990.077990.07799
process[Recruitment].ycs_values{1982}0.027510.027510.027510.032800.032800.027510.027510.02751
process[Recruitment].ycs_values{1983}0.112480.112480.112480.136470.136470.112480.112480.11248
process[Recruitment].ycs_values{1984}0.107570.107570.107570.130800.130800.107570.107570.10757
process[Recruitment].ycs_values{1985}0.092560.092560.092560.112560.112560.092560.092560.09256
process[Recruitment].ycs_values{1986}0.234740.234740.234740.286160.286160.234740.234740.23474
process[Recruitment].ycs_values{1987}0.105180.105180.105180.127930.127930.105180.105180.10518
process[Recruitment].ycs_values{1988}0.358490.358490.358490.437720.437720.358490.358490.35849
process[Recruitment].ycs_values{1989}0.030010.030010.030010.035900.035900.030010.030010.03001
process[Recruitment].ycs_values{1990}0.211600.211600.211600.256490.256490.211600.211600.21160
process[Recruitment].ycs_values{1991}2.268622.268622.268622.751162.751162.268622.268622.26862
process[Recruitment].ycs_values{1992}0.460420.460420.460420.558710.558710.460420.460420.46042
process[Recruitment].ycs_values{1993}0.218180.218180.218180.263900.263900.218180.218180.21818
process[Recruitment].ycs_values{1994}0.106320.106320.106320.126750.126750.106320.106320.10632
process[Recruitment].ycs_values{1995}0.462200.462200.462200.560020.560020.462200.462200.46220
process[Recruitment].ycs_values{1996}0.299580.299580.299580.361920.361920.299580.299580.29958
process[Recruitment].ycs_values{1997}0.120960.120960.120960.144860.144860.120960.120960.12096
process[Recruitment].ycs_values{1998}0.264760.264760.264760.320600.320600.264760.264760.26476
process[Recruitment].ycs_values{1999}0.160480.160480.160480.192790.192790.160480.160480.16048
process[Recruitment].ycs_values{2000}0.246240.246240.246240.298740.298740.246240.246240.24624
process[Recruitment].ycs_values{2001}0.574980.574980.574980.705180.705180.574980.574980.57498
process[Recruitment].ycs_values{2002}0.338160.338160.338160.417690.417690.338160.338160.33816
process[Recruitment].ycs_values{2003}0.205850.205850.205850.254270.254270.205850.205850.20585
process[Recruitment].ycs_values{2004}0.201740.201740.201740.252380.252380.201740.201740.20174
process[Recruitment].ycs_values{2005}0.256780.256780.256780.324950.324950.256780.256780.25678
process[Recruitment].ycs_values{2006}1.314091.314091.314091.695671.695671.314091.314091.31409
process[Recruitment].ycs_values{2007}0.523280.523280.523280.686600.686600.523280.523280.52328
process[Recruitment].ycs_values{2008}0.152420.152420.152420.200670.200670.152420.152420.15242
process[Recruitment].ycs_values{2009}0.876060.876060.876061.203721.203720.876060.876060.87606
process[Recruitment].ycs_values{2010}0.007720.007720.007720.169350.169350.007720.007720.00772
process[Recruitment].ycs_values{2011}0.590700.590700.590700.875690.875690.590700.590700.59070
process[Recruitment].ycs_values{2012}0.094950.094950.094950.132660.132660.094950.094950.09495
process[Instantaneous_Mortality].m{male.nonspawn}       0.157450.157450.157450.151180.151180.157450.157450.15745
process[Instantaneous_Mortality].m{female.nonspawn}       0.166510.166510.166510.160330.160330.166510.166510.16651
observation[TangaroaAcousticMature].process_error   0.000100.000100.000100.000100.000100.000100.000100.00010
Casal2 parameter estimates: Percent Difference from betadiff_casal_flags_on
rownamesbetadiff_casal_flags_onbetadiff_casal_flags_offbetadiff_casal_flags_on_low_tolcppad_casal_flags_oncppad_casal_flags_offadolc_casal_flags_onadolc_casal_flags_offadolc_casal_flags_on_low_tol
process[Recruitment].b0              0.0000.0000.000-4.979-4.9790.0000.0000.000
selectivity[MaturationSel_male].v{1}            0.0000.0000.000-0.254-0.2540.0000.0000.000
selectivity[MaturationSel_male].v{2}            0.0000.0000.0000.7250.7250.0000.0000.000
selectivity[MaturationSel_male].v{3}            0.0000.0000.0000.3210.3210.0000.0000.000
selectivity[MaturationSel_male].v{4}            0.0000.0000.000-12.654-12.6540.0000.0000.000
selectivity[MaturationSel_female].v{1}            0.0000.0000.000-0.211-0.2110.0000.0000.000
selectivity[MaturationSel_female].v{2}            0.0000.0000.0000.6010.6010.0000.0000.000
selectivity[MaturationSel_female].v{3}            0.0000.0000.0000.4840.4840.0000.0000.000
selectivity[MaturationSel_female].v{4}            0.0000.0000.0000.0000.0000.0000.0000.000
process[Recruitment].ycs_values{1958}0.0000.0000.000-1.673-1.6730.0000.0000.000
process[Recruitment].ycs_values{1959}0.0000.0000.000-1.847-1.8470.0000.0000.000
process[Recruitment].ycs_values{1960}0.0000.0000.000-2.036-2.0360.0000.0000.000
process[Recruitment].ycs_values{1961}0.0000.0000.000-2.242-2.2420.0000.0000.000
process[Recruitment].ycs_values{1962}0.0000.0000.000-2.479-2.4790.0000.0000.000
process[Recruitment].ycs_values{1963}0.0000.0000.000-2.703-2.7030.0000.0000.000
process[Recruitment].ycs_values{1964}0.0000.0000.000-2.902-2.9020.0000.0000.000
process[Recruitment].ycs_values{1965}0.0000.0000.000-16.643-16.6430.0000.0000.000
process[Recruitment].ycs_values{1966}0.0000.0000.000-14.570-14.5700.0000.0000.000
process[Recruitment].ycs_values{1967}0.0000.0000.000-14.993-14.9930.0000.0000.000
process[Recruitment].ycs_values{1968}0.0000.0000.000-15.121-15.1210.0000.0000.000
process[Recruitment].ycs_values{1969}0.0000.0000.000-14.081-14.0810.0000.0000.000
process[Recruitment].ycs_values{1970}0.0000.0000.000-13.297-13.2970.0000.0000.000
process[Recruitment].ycs_values{1971}0.0000.0000.000-16.229-16.2290.0000.0000.000
process[Recruitment].ycs_values{1972}0.0000.0000.000-16.169-16.1690.0000.0000.000
process[Recruitment].ycs_values{1973}0.0000.0000.000-15.536-15.5360.0000.0000.000
process[Recruitment].ycs_values{1974}0.0000.0000.000-16.571-16.5710.0000.0000.000
process[Recruitment].ycs_values{1975}0.0000.0000.000-18.367-18.3670.0000.0000.000
process[Recruitment].ycs_values{1976}0.0000.0000.000-17.388-17.3880.0000.0000.000
process[Recruitment].ycs_values{1977}0.0000.0000.000-17.382-17.3820.0000.0000.000
process[Recruitment].ycs_values{1978}0.0000.0000.000-18.215-18.2150.0000.0000.000
process[Recruitment].ycs_values{1979}0.0000.0000.000-20.174-20.1740.0000.0000.000
process[Recruitment].ycs_values{1980}0.0000.0000.000-20.787-20.7870.0000.0000.000
process[Recruitment].ycs_values{1981}0.0000.0000.000-20.557-20.5570.0000.0000.000
process[Recruitment].ycs_values{1982}0.0000.0000.000-19.235-19.2350.0000.0000.000
process[Recruitment].ycs_values{1983}0.0000.0000.000-21.335-21.3350.0000.0000.000
process[Recruitment].ycs_values{1984}0.0000.0000.000-21.601-21.6010.0000.0000.000
process[Recruitment].ycs_values{1985}0.0000.0000.000-21.613-21.6130.0000.0000.000
process[Recruitment].ycs_values{1986}0.0000.0000.000-21.907-21.9070.0000.0000.000
process[Recruitment].ycs_values{1987}0.0000.0000.000-21.632-21.6320.0000.0000.000
process[Recruitment].ycs_values{1988}0.0000.0000.000-22.100-22.1000.0000.0000.000
process[Recruitment].ycs_values{1989}0.0000.0000.000-19.633-19.6330.0000.0000.000
process[Recruitment].ycs_values{1990}0.0000.0000.000-21.217-21.2170.0000.0000.000
process[Recruitment].ycs_values{1991}0.0000.0000.000-21.270-21.2700.0000.0000.000
process[Recruitment].ycs_values{1992}0.0000.0000.000-21.350-21.3500.0000.0000.000
process[Recruitment].ycs_values{1993}0.0000.0000.000-20.955-20.9550.0000.0000.000
process[Recruitment].ycs_values{1994}0.0000.0000.000-19.208-19.2080.0000.0000.000
process[Recruitment].ycs_values{1995}0.0000.0000.000-21.162-21.1620.0000.0000.000
process[Recruitment].ycs_values{1996}0.0000.0000.000-20.809-20.8090.0000.0000.000
process[Recruitment].ycs_values{1997}0.0000.0000.000-19.754-19.7540.0000.0000.000
process[Recruitment].ycs_values{1998}0.0000.0000.000-21.087-21.0870.0000.0000.000
process[Recruitment].ycs_values{1999}0.0000.0000.000-20.132-20.1320.0000.0000.000
process[Recruitment].ycs_values{2000}0.0000.0000.000-21.324-21.3240.0000.0000.000
process[Recruitment].ycs_values{2001}0.0000.0000.000-22.645-22.6450.0000.0000.000
process[Recruitment].ycs_values{2002}0.0000.0000.000-23.517-23.5170.0000.0000.000
process[Recruitment].ycs_values{2003}0.0000.0000.000-23.521-23.5210.0000.0000.000
process[Recruitment].ycs_values{2004}0.0000.0000.000-25.098-25.0980.0000.0000.000
process[Recruitment].ycs_values{2005}0.0000.0000.000-26.551-26.5510.0000.0000.000
process[Recruitment].ycs_values{2006}0.0000.0000.000-29.038-29.0380.0000.0000.000
process[Recruitment].ycs_values{2007}0.0000.0000.000-31.210-31.2100.0000.0000.000
process[Recruitment].ycs_values{2008}0.0000.0000.000-31.658-31.6580.0000.0000.000
process[Recruitment].ycs_values{2009}0.0000.0000.000-37.401-37.4010.0000.0000.000
process[Recruitment].ycs_values{2010}0.0000.0000.000-2093.890-2093.8900.0000.0000.000
process[Recruitment].ycs_values{2011}0.0000.0000.000-48.246-48.2460.0000.0000.000
process[Recruitment].ycs_values{2012}0.0000.0000.000-39.718-39.7180.0000.0000.000
process[Instantaneous_Mortality].m{male.nonspawn}       0.0000.0000.0003.9783.9780.0000.0000.000
process[Instantaneous_Mortality].m{female.nonspawn}       0.0000.0000.0003.7133.7130.0000.0000.000
observation[TangaroaAcousticMature].process_error   0.0000.0000.0000.0000.0000.0000.0000.000

CASAL objective function component values
ComponentBase_ModelSensitivity_1
TangaroaAcousticImmature17.98017.980
TangaroaAcousticMature-9.196-9.196
ObserverProportionsAtAge957.800957.800
prior_on_initialization.B012.66012.660
prior_on_relative_abundance[TangaroaAcousticMature].cv_process_error-9.210-9.210
prior_on_natural_mortality.avg-1.183-1.183
prior_on_natural_mortality.diff0.0170.017
prior_on_migration[toSpawn].rates_male0.0000.000
prior_on_migration[toSpawn].rates_female0.0000.000
prior_on_recruitment.YCS-30.170-30.170
prior_on_q_TangaroaImmatureq0.0000.000
prior_on_q_TangaroaMatureq-0.732-0.732
Penalty-CatchLimitTrawl0.0000.000
Penalty-YCS0.3970.397
Total938.400938.400
Casal2 objective function component values
rownamesbetadiff_casal_flags_onbetadiff_casal_flags_offbetadiff_casal_flags_on_low_tolcppad_casal_flags_oncppad_casal_flags_offadolc_casal_flags_onadolc_casal_flags_offadolc_casal_flags_on_low_tol
observation->TangaroaAcousticMature-1993                 -1.281-1.281-1.281-1.371-1.371-1.281-1.281-1.281
observation->TangaroaAcousticMature-1994                 -0.601-0.601-0.601-0.439-0.439-0.601-0.601-0.601
observation->TangaroaAcousticMature-1995                 -0.448-0.448-0.448-0.622-0.622-0.448-0.448-0.448
observation->TangaroaAcousticMature-1998                 -1.707-1.707-1.707-1.531-1.531-1.707-1.707-1.707
observation->TangaroaAcousticMature-2000                 -1.778-1.778-1.778-1.764-1.764-1.778-1.778-1.778
observation->TangaroaAcousticMature-2002                 -0.369-0.369-0.369-0.358-0.358-0.369-0.369-0.369
observation->TangaroaAcousticMature-2004                 -0.784-0.784-0.784-0.807-0.807-0.784-0.784-0.784
observation->TangaroaAcousticMature-2006                 -0.888-0.888-0.888-0.881-0.881-0.888-0.888-0.888
observation->TangaroaAcousticMature-2009                 0.6990.6990.6990.4550.4550.6990.6990.699
observation->TangaroaAcousticMature-2011                 -1.004-1.004-1.004-0.638-0.638-1.004-1.004-1.004
observation->TangaroaAcousticMature-2013                 -1.401-1.401-1.401-1.239-1.239-1.401-1.401-1.401
observation->TangaroaAcousticImmature-1993                 1.9681.9681.9682.5422.5421.9681.9681.968
observation->TangaroaAcousticImmature-1994                 0.8170.8170.8170.6180.6180.8170.8170.817
observation->TangaroaAcousticImmature-1995                 1.9451.9451.9452.1992.1991.9451.9451.945
observation->TangaroaAcousticImmature-1998                 -1.536-1.536-1.536-1.444-1.444-1.536-1.536-1.536
observation->TangaroaAcousticImmature-2000                 4.8664.8664.8664.3064.3064.8664.8664.866
observation->TangaroaAcousticImmature-2002                 7.3217.3217.3217.1227.1227.3217.3217.321
observation->TangaroaAcousticImmature-2004                 1.7221.7221.7221.4301.4301.7221.7221.722
observation->TangaroaAcousticImmature-2006                 -0.467-0.467-0.467-0.524-0.524-0.467-0.467-0.467
observation->TangaroaAcousticImmature-2009                 2.2212.2212.2211.8451.8452.2212.2212.221
observation->TangaroaAcousticImmature-2011                 1.5431.5431.5430.5140.5141.5431.5431.543
observation->TangaroaAcousticImmature-2013                 -0.388-0.388-0.388-0.628-0.628-0.388-0.388-0.388
observation->ObserverProportionsAtAge-1979                 15.19815.19815.19815.17015.17015.19815.19815.198
observation->ObserverProportionsAtAge-1980                 17.07617.07617.07616.99716.99717.07617.07617.076
observation->ObserverProportionsAtAge-1981                 30.96130.96130.96130.81630.81630.96130.96130.961
observation->ObserverProportionsAtAge-1982                 26.03026.03026.03025.98825.98826.03026.03026.030
observation->ObserverProportionsAtAge-1983                 20.42320.42320.42320.40520.40520.42320.42320.423
observation->ObserverProportionsAtAge-1984                 26.17426.17426.17426.18826.18826.17426.17426.174
observation->ObserverProportionsAtAge-1985                 22.91722.91722.91722.92522.92522.91722.91722.917
observation->ObserverProportionsAtAge-1986                 27.62827.62827.62827.66627.66627.62827.62827.628
observation->ObserverProportionsAtAge-1987                 28.82528.82528.82528.85228.85228.82528.82528.825
observation->ObserverProportionsAtAge-1988                 28.86228.86228.86228.85228.85228.86228.86228.862
observation->ObserverProportionsAtAge-1989                 31.71331.71331.71331.66431.66431.71331.71331.713
observation->ObserverProportionsAtAge-1990                 28.18728.18728.18728.16728.16728.18728.18728.187
observation->ObserverProportionsAtAge-1991                 37.65937.65937.65937.70137.70137.65937.65937.659
observation->ObserverProportionsAtAge-1992                 28.02628.02628.02628.00528.00528.02628.02628.026
observation->ObserverProportionsAtAge-1993                 29.23229.23229.23229.21829.21829.23229.23229.232
observation->ObserverProportionsAtAge-1994                 22.14222.14222.14222.18222.18222.14222.14222.142
observation->ObserverProportionsAtAge-1995                 21.90921.90921.90921.88021.88021.90921.90921.909
observation->ObserverProportionsAtAge-1996                 25.89825.89825.89825.95725.95725.89825.89825.898
observation->ObserverProportionsAtAge-1997                 21.10421.10421.10421.12121.12121.10421.10421.104
observation->ObserverProportionsAtAge-1998                 20.38420.38420.38420.36620.36620.38420.38420.384
observation->ObserverProportionsAtAge-1999                 24.42224.42224.42224.46224.46224.42224.42224.422
observation->ObserverProportionsAtAge-2000                 16.71916.71916.71916.75916.75916.71916.71916.719
observation->ObserverProportionsAtAge-2001                 26.26826.26826.26826.42226.42226.26826.26826.268
observation->ObserverProportionsAtAge-2002                 20.04920.04920.04920.05820.05820.04920.04920.049
observation->ObserverProportionsAtAge-2003                 34.05334.05334.05333.94133.94134.05334.05334.053
observation->ObserverProportionsAtAge-2004                 18.37618.37618.37618.36918.36918.37618.37618.376
observation->ObserverProportionsAtAge-2005                 27.99327.99327.99328.12328.12327.99327.99327.993
observation->ObserverProportionsAtAge-2006                 23.33023.33023.33023.29923.29923.33023.33023.330
observation->ObserverProportionsAtAge-2007                 26.65226.65226.65226.68526.68526.65226.65226.652
observation->ObserverProportionsAtAge-2008                 37.88637.88637.88637.85837.85837.88637.88637.886
observation->ObserverProportionsAtAge-2009                 20.40420.40420.40420.37520.37520.40420.40420.404
observation->ObserverProportionsAtAge-2010                 27.64627.64627.64627.66027.66027.64627.64627.646
observation->ObserverProportionsAtAge-2011                 25.05025.05025.05025.08725.08725.05025.05025.050
observation->ObserverProportionsAtAge-2012                 27.28327.28327.28326.83626.83627.28327.28327.283
observation->ObserverProportionsAtAge-2013                 25.15525.15525.15527.97627.97625.15525.15525.155
observation->ObserverProportionsAtAge-2014                 49.11749.11749.11735.39535.39549.11749.11749.117
observation->ObserverProportionsAtAge-2015                 34.20334.20334.20328.36228.36234.20334.20334.203
prior->B0->process[Recruitment].b0              12.61012.61012.61012.65912.65912.61012.61012.610
prior->Migration_male->selectivity[MaturationSel_male].v{1}            0.0000.0000.0000.0000.0000.0000.0000.000
prior->Migration_male->selectivity[MaturationSel_male].v{2}            0.0000.0000.0000.0000.0000.0000.0000.000
prior->Migration_male->selectivity[MaturationSel_male].v{3}            0.0000.0000.0000.0000.0000.0000.0000.000
prior->Migration_male->selectivity[MaturationSel_male].v{4}            0.0000.0000.0000.0000.0000.0000.0000.000
prior->Migration_female->selectivity[MaturationSel_female].v{1}            0.0000.0000.0000.0000.0000.0000.0000.000
prior->Migration_female->selectivity[MaturationSel_female].v{2}            0.0000.0000.0000.0000.0000.0000.0000.000
prior->Migration_female->selectivity[MaturationSel_female].v{3}            0.0000.0000.0000.0000.0000.0000.0000.000
prior->Migration_female->selectivity[MaturationSel_female].v{4}            0.0000.0000.0000.0000.0000.0000.0000.000
prior->YCS->process[Recruitment].ycs_values{1958}-0.984-0.984-0.984-0.982-0.982-0.984-0.984-0.984
prior->YCS->process[Recruitment].ycs_values{1959}-0.982-0.982-0.982-0.979-0.979-0.982-0.982-0.982
prior->YCS->process[Recruitment].ycs_values{1960}-0.979-0.979-0.979-0.976-0.976-0.979-0.979-0.979
prior->YCS->process[Recruitment].ycs_values{1961}-0.975-0.975-0.975-0.971-0.971-0.975-0.975-0.975
prior->YCS->process[Recruitment].ycs_values{1962}-0.970-0.970-0.970-0.965-0.965-0.970-0.970-0.970
prior->YCS->process[Recruitment].ycs_values{1963}-0.962-0.962-0.962-0.955-0.955-0.962-0.962-0.962
prior->YCS->process[Recruitment].ycs_values{1964}-0.950-0.950-0.950-0.941-0.941-0.950-0.950-0.950
prior->YCS->process[Recruitment].ycs_values{1965}-0.336-0.336-0.336-0.147-0.147-0.336-0.336-0.336
prior->YCS->process[Recruitment].ycs_values{1966}-0.730-0.730-0.730-0.622-0.622-0.730-0.730-0.730
prior->YCS->process[Recruitment].ycs_values{1967}-0.927-0.927-0.927-0.867-0.867-0.927-0.927-0.927
prior->YCS->process[Recruitment].ycs_values{1968}-0.989-0.989-0.989-0.976-0.976-0.989-0.989-0.989
prior->YCS->process[Recruitment].ycs_values{1969}-0.793-0.793-0.793-0.867-0.867-0.793-0.793-0.793
prior->YCS->process[Recruitment].ycs_values{1970}-0.306-0.306-0.306-0.445-0.445-0.306-0.306-0.306
prior->YCS->process[Recruitment].ycs_values{1971}-0.858-0.858-0.858-0.924-0.924-0.858-0.858-0.858
prior->YCS->process[Recruitment].ycs_values{1972}-0.574-0.574-0.574-0.700-0.700-0.574-0.574-0.574
prior->YCS->process[Recruitment].ycs_values{1973}0.1700.1700.170-0.041-0.0410.1700.1700.170
prior->YCS->process[Recruitment].ycs_values{1974}0.1010.1010.101-0.115-0.1150.1010.1010.101
prior->YCS->process[Recruitment].ycs_values{1975}-0.708-0.708-0.708-0.821-0.821-0.708-0.708-0.708
prior->YCS->process[Recruitment].ycs_values{1976}0.4040.4040.4040.1480.1480.4040.4040.404
prior->YCS->process[Recruitment].ycs_values{1977}0.8440.8440.8440.5490.5490.8440.8440.844
prior->YCS->process[Recruitment].ycs_values{1978}0.4360.4360.4360.1660.1660.4360.4360.436
prior->YCS->process[Recruitment].ycs_values{1979}-0.937-0.937-0.937-0.860-0.860-0.937-0.937-0.937
prior->YCS->process[Recruitment].ycs_values{1980}-0.945-0.945-0.945-0.871-0.871-0.945-0.945-0.945
prior->YCS->process[Recruitment].ycs_values{1981}-0.414-0.414-0.414-0.598-0.598-0.414-0.414-0.414
prior->YCS->process[Recruitment].ycs_values{1982}1.2581.2581.2580.8980.8981.2581.2581.258
prior->YCS->process[Recruitment].ycs_values{1983}-0.741-0.741-0.741-0.859-0.859-0.741-0.741-0.741
prior->YCS->process[Recruitment].ycs_values{1984}-0.709-0.709-0.709-0.837-0.837-0.709-0.709-0.709
prior->YCS->process[Recruitment].ycs_values{1985}-0.584-0.584-0.584-0.742-0.742-0.584-0.584-0.584
prior->YCS->process[Recruitment].ycs_values{1986}-0.989-0.989-0.989-0.962-0.962-0.989-0.989-0.989
prior->YCS->process[Recruitment].ycs_values{1987}-0.692-0.692-0.692-0.824-0.824-0.692-0.692-0.692
prior->YCS->process[Recruitment].ycs_values{1988}-0.883-0.883-0.883-0.771-0.771-0.883-0.883-0.883
prior->YCS->process[Recruitment].ycs_values{1989}1.0761.0761.0760.7260.7261.0761.0761.076
prior->YCS->process[Recruitment].ycs_values{1990}-0.987-0.987-0.987-0.982-0.982-0.987-0.987-0.987
prior->YCS->process[Recruitment].ycs_values{1991}1.6921.6921.6922.1592.1591.6921.6921.692
prior->YCS->process[Recruitment].ycs_values{1992}-0.736-0.736-0.736-0.578-0.578-0.736-0.736-0.736
prior->YCS->process[Recruitment].ycs_values{1993}-0.989-0.989-0.989-0.978-0.978-0.989-0.989-0.989
prior->YCS->process[Recruitment].ycs_values{1994}-0.700-0.700-0.700-0.819-0.819-0.700-0.700-0.700
prior->YCS->process[Recruitment].ycs_values{1995}-0.733-0.733-0.733-0.576-0.576-0.733-0.733-0.733
prior->YCS->process[Recruitment].ycs_values{1996}-0.950-0.950-0.950-0.879-0.879-0.950-0.950-0.950
prior->YCS->process[Recruitment].ycs_values{1997}-0.790-0.790-0.790-0.888-0.888-0.790-0.790-0.790
prior->YCS->process[Recruitment].ycs_values{1998}-0.977-0.977-0.977-0.929-0.929-0.977-0.977-0.977
prior->YCS->process[Recruitment].ycs_values{1999}-0.929-0.929-0.929-0.976-0.976-0.929-0.929-0.929
prior->YCS->process[Recruitment].ycs_values{2000}-0.986-0.986-0.986-0.951-0.951-0.986-0.986-0.986
prior->YCS->process[Recruitment].ycs_values{2001}-0.552-0.552-0.552-0.339-0.339-0.552-0.552-0.552
prior->YCS->process[Recruitment].ycs_values{2002}-0.909-0.909-0.909-0.801-0.801-0.909-0.909-0.909
prior->YCS->process[Recruitment].ycs_values{2003}-0.985-0.985-0.985-0.983-0.983-0.985-0.985-0.985
prior->YCS->process[Recruitment].ycs_values{2004}-0.983-0.983-0.983-0.984-0.984-0.983-0.983-0.983
prior->YCS->process[Recruitment].ycs_values{2005}-0.982-0.982-0.982-0.924-0.924-0.982-0.982-0.982
prior->YCS->process[Recruitment].ycs_values{2006}0.5710.5710.5711.0571.0570.5710.5710.571
prior->YCS->process[Recruitment].ycs_values{2007}-0.636-0.636-0.636-0.369-0.369-0.636-0.636-0.636
prior->YCS->process[Recruitment].ycs_values{2008}-0.910-0.910-0.910-0.982-0.982-0.910-0.910-0.910
prior->YCS->process[Recruitment].ycs_values{2009}-0.066-0.066-0.0660.4190.419-0.066-0.066-0.066
prior->YCS->process[Recruitment].ycs_values{2010}4.7824.7824.782-0.947-0.9474.7824.7824.782
prior->YCS->process[Recruitment].ycs_values{2011}-0.526-0.526-0.526-0.067-0.067-0.526-0.526-0.526
prior->YCS->process[Recruitment].ycs_values{2012}-0.607-0.607-0.607-0.845-0.845-0.607-0.607-0.607
prior->M_male_with_avg_prior->process[Instantaneous_Mortality].m{male.nonspawn}       -1.354-1.354-1.354-1.183-1.183-1.354-1.354-1.354
prior->M_female_with_diff_prior->process[Instantaneous_Mortality].m{female.nonspawn}       0.0160.0160.0160.0170.0170.0160.0160.016
prior->mature_process_error->observation[TangaroaAcousticMature].process_error   -9.210-9.210-9.210-9.210-9.210-9.210-9.210-9.210
additional_prior->Penalty-YCS                 0.4830.4830.4830.3970.3970.4830.4830.483
additional_prior->TangaroaMatureq                 -0.713-0.713-0.713-0.732-0.732-0.713-0.713-0.713
jacobian->avg_diff                 0.0000.0000.0000.0000.0000.0000.0000.000
total_negloglike                 962.721962.721962.721938.228938.228962.721962.721962.721

## [1] "CASAL base model convergence information"
## [1] "Minimiser convergence threshold: 2e-006"                                                                  
## [2] "fmm: have converged: t = 1.56689e-006 f = 938.352"                                                        
## [3] "Successful convergence in optimise"                                                                       
## [4] "Minimiser achieved convergence after 260 quasi-Newton iterations using 321 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-009"                                                                                 
## [2] "fmm: step size too small. Indicates successful convergence (though this is not the textbook ideal convergence situation)"
## [3] "Successful convergence in optimise"                                                                                      
## [4] "Minimiser achieved convergence after 270 quasi-Newton iterations using 338 objective function evaluations"               
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 1.7148e-07 f = 973.615"
## [2] "Successful convergence in optimise"             
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 1.40909e-07 f = 973.615"
## [2] "Successful convergence in optimise"              
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: step size too small. Indicates successful convergence (though this is not the textbook ideal convergence situation)"
## [2] "Successful convergence in optimise"                                                                                      
## [1] ""
## [1] "Casal2 cppad_casal_flags_on model convergence information"
##  [1] "Number of nonzeros in equality constraint Jacobian...:        0"
##  [2] "Number of nonzeros in inequality constraint Jacobian.:       67"
##  [3] "Number of nonzeros in Lagrangian Hessian.............:     2278"
##  [4] "Number of Iterations....: 66"                                   
##  [5] "Number of objective function evaluations             = 89"      
##  [6] "Number of objective gradient evaluations             = 67"      
##  [7] "Number of equality constraint evaluations            = 0"       
##  [8] "Number of inequality constraint evaluations          = 89"      
##  [9] "Number of equality constraint Jacobian evaluations   = 0"       
## [10] "Number of inequality constraint Jacobian evaluations = 67"      
## [11] "Number of Lagrangian Hessian evaluations             = 66"      
## [12] "EXIT: Optimal Solution Found."                                  
## [13] "Number of nonzeros in equality constraint Jacobian...:        0"
## [14] "Number of nonzeros in inequality constraint Jacobian.:       67"
## [15] "Number of nonzeros in Lagrangian Hessian.............:     2278"
## [16] "Number of Iterations....: 29"                                   
## [17] "Number of objective function evaluations             = 44"      
## [18] "Number of objective gradient evaluations             = 30"      
## [19] "Number of equality constraint evaluations            = 0"       
## [20] "Number of inequality constraint evaluations          = 44"      
## [21] "Number of equality constraint Jacobian evaluations   = 0"       
## [22] "Number of inequality constraint Jacobian evaluations = 30"      
## [23] "Number of Lagrangian Hessian evaluations             = 29"      
## [24] "EXIT: Optimal Solution Found."                                  
## [1] ""
## [1] "Casal2 cppad_casal_flags_off model convergence information"
##  [1] "Number of nonzeros in equality constraint Jacobian...:        0"
##  [2] "Number of nonzeros in inequality constraint Jacobian.:       67"
##  [3] "Number of nonzeros in Lagrangian Hessian.............:     2278"
##  [4] "Number of Iterations....: 66"                                   
##  [5] "Number of objective function evaluations             = 89"      
##  [6] "Number of objective gradient evaluations             = 67"      
##  [7] "Number of equality constraint evaluations            = 0"       
##  [8] "Number of inequality constraint evaluations          = 89"      
##  [9] "Number of equality constraint Jacobian evaluations   = 0"       
## [10] "Number of inequality constraint Jacobian evaluations = 67"      
## [11] "Number of Lagrangian Hessian evaluations             = 66"      
## [12] "EXIT: Optimal Solution Found."                                  
## [13] "Number of nonzeros in equality constraint Jacobian...:        0"
## [14] "Number of nonzeros in inequality constraint Jacobian.:       67"
## [15] "Number of nonzeros in Lagrangian Hessian.............:     2278"
## [16] "Number of Iterations....: 29"                                   
## [17] "Number of objective function evaluations             = 44"      
## [18] "Number of objective gradient evaluations             = 30"      
## [19] "Number of equality constraint evaluations            = 0"       
## [20] "Number of inequality constraint evaluations          = 44"      
## [21] "Number of equality constraint Jacobian evaluations   = 0"       
## [22] "Number of inequality constraint Jacobian evaluations = 30"      
## [23] "Number of Lagrangian Hessian evaluations             = 29"      
## [24] "EXIT: Optimal Solution Found."                                  
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model convergence information"
## character(0)
## [1] "CASAL model warnings"
##                                                      parameter estimate
## 1  relative_abundance[TangaroaAcousticMature].cv_process_error   0.0001
## 2                           migration[toSpawn].rates_female[4]    0.999
## 3                                          recruitment.YCS[13]  0.08025
## 4                                          recruitment.YCS[16]  0.05757
## 5                                          recruitment.YCS[17]  0.06079
## 6                                          recruitment.YCS[19]  0.05057
## 7                                          recruitment.YCS[20]  0.03959
## 8                                          recruitment.YCS[21]  0.04996
## 9                                          recruitment.YCS[24]  0.09402
## 10                                         recruitment.YCS[25]   0.0328
## 11                                         recruitment.YCS[32]   0.0359
##    lower.bound upper.bound
## 1       0.0001           1
## 2        0.001       0.999
## 3        0.001         100
## 4        0.001         100
## 5        0.001         100
## 6        0.001         100
## 7        0.001         100
## 8        0.001         100
## 9        0.001         100
## 10       0.001         100
## 11       0.001         100
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
##                                                      parameter estimate
## 1  relative_abundance[TangaroaAcousticMature].cv_process_error   0.0001
## 2                           migration[toSpawn].rates_female[4]    0.999
## 3                                          recruitment.YCS[13]  0.08025
## 4                                          recruitment.YCS[16]  0.05757
## 5                                          recruitment.YCS[17]  0.06079
## 6                                          recruitment.YCS[19]  0.05057
## 7                                          recruitment.YCS[20]  0.03959
## 8                                          recruitment.YCS[21]  0.04996
## 9                                          recruitment.YCS[24]  0.09402
## 10                                         recruitment.YCS[25]   0.0328
## 11                                         recruitment.YCS[32]   0.0359
##    lower.bound upper.bound
## 1       0.0001           1
## 2        0.001       0.999
## 3        0.001         100
## 4        0.001         100
## 5        0.001         100
## 6        0.001         100
## 7        0.001         100
## 8        0.001         100
## 9        0.001         100
## 10       0.001         100
## 11       0.001         100
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 cppad_casal_flags_on model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 cppad_casal_flags_off model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"
## 
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model warnings"
## $warnings_found
## [1] 4
## 
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
## 
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
## 
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
## 
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
## 
## $type
## [1] "warnings"

1.5 Matching of outputs

Time series comparisons with CASAL base model results

## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run cppad_casal_flags_on"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run cppad_casal_flags_off"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_off"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on_low_tol"
## [1] "Actual catches for Trawl match: yes"
## [1] ""

Derived quantities

SB0, SBcurrent, MSY, F_MSY, others...

1.6 Plots

Comparison plots

## [1] "CASAL base parameter correlation range (excluding 1.0): -0.5771 0.7601"

## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.465 0.7616"
## Warning in min(x): no non-missing arguments to min; returning Inf
## Warning in max(x): no non-missing arguments to max; returning -Inf

## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): Inf -Inf"

## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.474750601346601 0.754913095502236"

## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.828728281162341 0.771401949199379"

## [1] "Casal2 cppad_casal_flags_on parameter correlation range (excluding 1.0): -0.927410854513845 0.766116145794423"

## [1] "Casal2 cppad_casal_flags_off parameter correlation range (excluding 1.0): -0.927410854513845 0.766116145794423"

## [1] "Casal2 adolc_casal_flags_on parameter correlation range (excluding 1.0): -0.449867451595697 0.765859852647084"

## [1] "Casal2 adolc_casal_flags_off parameter correlation range (excluding 1.0): -0.475954909278459 0.77245952551618"

## [1] "Casal2 adolc_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.450174071110356 0.76519971244179"